Nothing
# Single season occupancy with no covariates (psi(.) p(.) model)
# 'link' argument added 2015-02-20
occSS0 <-
function(y, n, ci=0.95, link=c("logit", "probit"), ...) {
# n is a vector with the number of occasions at each site.
# y is a vector with the number of detections at each site.
# ci is the required confidence interval.
if(length(n) == 1)
n <- rep(n, length(y))
if(length(y) != length(n))
stop("y and n must have the same length")
if(any(y > n))
stop("y cannot be greater than n")
crit <- fixCI(ci)
if(match.arg(link) == "logit") {
plink <- plogis
} else {
plink <- pnorm
}
beta.mat <- matrix(NA_real_, 2, 4)
colnames(beta.mat) <- c("est", "SE", "lowCI", "uppCI")
rownames(beta.mat) <- c("psiHat", "pHat")
logLik <- NA_real_
npar <- NA_integer_
varcov <- NULL
if(sum(n) > 0) { # If all n's are 0, no data available.
nll <- function(params) {
logpsi <- plink(params[1], log.p=TRUE)
log1mpsi <- plink( -params[1], log.p=TRUE)
logp <- plink(params[2], log.p=TRUE)
log1mp <- plink( -params[2], log.p=TRUE)
logprob <- logAddExp(logpsi + logp * y + log1mp * (n - y),
log1mpsi + log(y==0))
return(min(-sum(logprob), .Machine$double.xmax))
}
# res <- nlm(nll, params, hessian=TRUE)
nlmArgs <- list(...)
nlmArgs$f <- nll
nlmArgs$p <- rep(0, 2)
nlmArgs$hessian <- TRUE
res <- do.call(nlm, nlmArgs)
if(res$code > 2) # exit code 1 or 2 is ok.
warning(paste("Convergence may not have been reached (code", res$code, ")"))
beta.mat[,1] <- res$estimate
logLik <- -res$minimum
varcov0 <- try(chol2inv(chol(res$hessian)), silent=TRUE)
if (!inherits(varcov0, "try-error")) {
npar <- 2L
varcov <- varcov0
beta.mat[, 2] <- suppressWarnings(sqrt(diag(varcov)))
beta.mat[, 3:4] <- sweep(outer(beta.mat[, 2], crit), 1, res$estimate, "+")
}
}
out <- list(call = match.call(),
link = match.arg(link),
beta = beta.mat,
beta.vcv = varcov,
real = plink(beta.mat[, -2]),
logLik = c(logLik=logLik, df=npar, nobs=length(y)),
ci = ci,
formulae = list(psi= ~ 1, p = ~1),
index = list(psi= 1, p = 2))
class(out) <- c("wiqid", "list")
return(out)
}
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